On Friday 16 October 2009 15:49:16 Demet Arac-Ozkan wrote:
> Dear All,
>
> I have a few questions about protein structure and fold. I will appreciate your suggestions:
> We have the crystal structure of a protein and it looks like it might be a new domain.
>
> 1) Our structure looks like there are two domains however there are some close interactions
> between the two so we are not sure if we should define it as a single domain or two domains.
> I am looking for a program where I can enter a pdb file and get out domain boundaries based
> on the structure.
TLSMD analysis is a possibility.
It will not give a definitive answer to the question "one domain or two?",
but it may tell you where the boundary should be drawn if you do decide
to treat it as two.
http://skuld.bmsc.washington.edu/~tlsmd/
> For example something that can do a dot plot of the distances between residues?
>
> 2) We are wondering whether distant homologues of this protein also have this domain however sequence alignments are not reliable because there is little sequence identity. For doing structure-based sequence alignments, which programs can be used (other than SALIGN)?
>
> 3) What is the best way to decide whether a structure contains a new fold or not? For example if DALI z scores are about 8 (half of the domain is similar to one protein, the other half is similar to another protein), would you call it a new fold?
>
> Thanks a lot in advance,
>
> Demet Arac
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
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